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1.
BMC Genomics ; 23(1): 18, 2022 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-34983397

RESUMO

BACKGROUND: Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum. RESULTS: We found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato. CONCLUSIONS: Overall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.


Assuntos
Arabidopsis , Redes Reguladoras de Genes , Arabidopsis/genética , Elementos de DNA Transponíveis/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta
2.
BMC Genomics ; 23(1): 44, 2022 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-35012466

RESUMO

BACKGROUND: Small RNAs (sRNAs) regulate numerous plant processes directly related to yield, such as disease resistance and plant growth. To exploit this yield-regulating potential of sRNAs, the sRNA profile of one of the world's most important staple crops - rice - was investigated throughout plant development using next-generation sequencing. RESULTS: Root and leaves were investigated at both the vegetative and generative phase, and early-life sRNA expression was characterized in the embryo and endosperm. This led to the identification of 49,505 novel sRNAs and 5581 tRNA-derived sRNAs (tsRNAs). In all tissues, 24 nt small interfering RNAs (siRNAs) were highly expressed and associated with euchromatic, but not heterochromatic transposable elements. Twenty-one nt siRNAs deriving from genic regions in the endosperm were exceptionally highly expressed, mimicking previously reported expression levels of 24 nt siRNAs in younger endosperm samples. In rice embryos, sRNA content was highly diverse while tsRNAs were underrepresented, possibly due to snoRNA activity. Publicly available mRNA expression and DNA methylation profiles were used to identify putative siRNA targets in embryo and endosperm. These include multiple genes related to the plant hormones gibberellic acid and ethylene, and to seed phytoalexin and iron content. CONCLUSIONS: This work introduces multiple sRNAs as potential regulators of rice yield and quality, identifying them as possible targets for the continuous search to optimize rice production.


Assuntos
Oryza , Elementos de DNA Transponíveis , Endosperma , Regulação da Expressão Gênica de Plantas , Oryza/genética , Desenvolvimento Vegetal , RNA de Plantas , RNA Interferente Pequeno , Sementes
3.
Gene ; 809: 146015, 2022 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-34655721

RESUMO

This manuscript presents a method to systematically study intragenic variations in codon usage using correspondence analysis and the effective number of codons. The method is applied to >1100 proteobacteria. Codon usage biases (measured as inertia) increases with genome size, the same is true for the percentage of inertia explained by the first axis. It is shown that there is often a relaxed or more uniform codon usage near the gene termini. Ithis is not seen n small genomes, notably those of intracellular organisms like Buchnera aphidicola or Rickettsia prowazekii where translational selection plays less of a role. When genes from E. coli, for which translational selection is well described, are split into low, intermediate and high expression, respectively, it is shown that the intragenic codon usage pattern with more uniform usage at termini exist across all three expression groups. Furthermore, the correspondence analysis reveals a unique pattern in Bordetella pertussis due to IS expansion. This study thus shows that translational selection, genome shrinkage and IS expansion result in characteristic patterns in intragenic codon usage.


Assuntos
Uso do Códon , Elementos de DNA Transponíveis/genética , Proteobactérias/genética , Escherichia coli/genética , Genoma Bacteriano , Genômica/métodos , Biossíntese de Proteínas
4.
Methods Mol Biol ; 2377: 159-178, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709616

RESUMO

One of the most powerful approaches to detect the loci that enable a pathogen to cause disease is the creation of a high-density transposon mutant library by transposon insertion sequencing (TIS) and the screening of the library using an adequate in vivo and/or ex vivo model of the disease. Here we describe the procedure for detection of the putative loci required for a septicemic pathogen to cause sepsis in humans by using TIS plus an ex vivo model of septicaemia: to grow the pathogen in fresh and inactivated human serum. We selected V. vulnificus because it is a highly invasive pathogen capable of spreading from an infection site to the bloodstream, causing sepsis and death in less than 24 h. To survive and proliferate in blood (or host serum), the pathogen requires mechanisms to overcome the innate immune defenses and metabolic limitations of this host niche. Initially, genes under-represented for insertions can be used to estimate the V. vulnificus essential gene set. Analysis of the relative abundance of insertion mutants in the library after exposure to serum would detect which genes are essential for the pathogen to overcome the diverse limitations imposed by serum.


Assuntos
Vibrio vulnificus , Elementos de DNA Transponíveis/genética , Biblioteca Gênica , Humanos , Sepse/genética , Soro , Vibrio vulnificus/genética
5.
Methods Mol Biol ; 2377: 179-197, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709617

RESUMO

Transposon-insertion sequencing (Tn-Seq) allows for identification of bacterial genes and pathways essential for growth under a given condition. A transposon mutant is created by the stable and random integration of a transposable element into a genome of interest, followed by a period of outgrowth and selection for relative fitness on one or more growth media. By pooling hundreds of thousands of mutants, sequencing the transposon-genomic DNA junctions, and mapping sequencing reads to the genome, one can identify an abundance of reads in nonessential insertion regions and the absence of reads in essential regions and thus identify which genes are essential for a given growth condition. By performing this method iteratively across multiple strains and growth conditions, one can define a core essential genome for a species. Here, we describe this methodology in detail and its application for the species Pseudomonas aeruginosa, from generating mutants to the analysis of nonessential versus essential genes using the freely available software "FiTnEss".


Assuntos
Pseudomonas aeruginosa , Elementos de DNA Transponíveis/genética , Genes Bacterianos , Genes Essenciais , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Mutagênese Insercional , Pseudomonas aeruginosa/genética
6.
Virology ; 565: 52-57, 2022 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-34736160

RESUMO

Transposons are mobile DNAs that can move to different locations in host genomes. The integration site selection of transposons is critical for both themselves and host cells. Studies on the integration of retrotransposons and retroviruses have focused more on the global preference than on the local preference. The local preferences of retrotransposons are usually weak and of large diversity. Here, we analyzed hundreds of thousands of independent integration events of the Tf1 retrotransposon in Schizosaccharomyces pombe. The consensus sequence at the Tf1 integration sites shows a palindromic pattern, which can be divided into four sections, each of them contains one or more CGnTA units with a period of 10 base pairs, indicating interaction with subunits of the integrase oligomer in the pre-integration complex. Moreover, the analysis on the nucleosome occupancy flanking Tf1 target sites shows that Tf1 integration favors regions with one entire nucleosome depletion.


Assuntos
Elementos de DNA Transponíveis , Nucleossomos/metabolismo , Recombinação Genética , Retroelementos , Retroviridae/genética , Schizosaccharomyces/genética , Sequência Consenso , DNA Fúngico , Integrases/metabolismo , Sequências Repetidas Invertidas , Schizosaccharomyces/metabolismo
7.
Gene ; 808: 145975, 2022 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-34592349

RESUMO

Transposons are repetitive DNA sequences encompassing about half of the human genome. They play a vital role in genome stability maintenance and contribute to genomic diversity and evolution. Their activity is regulated by various mechanisms considering the deleterious effects of these mobile elements. Various genetic risk factors and environmental stress conditions affect the regulatory pathways causing alteration of transposon expression. Our knowledge of the biological role of transposons is limited especially in various types of cancers. Retrotransposons of different types (LTR-retrotransposons, LINEs and SINEs) regulate a plethora of genes that have a role in cell reprogramming, tumor suppression, cell cycle, apoptosis, cell adhesion and migration, and DNA repair. The regulatory mechanisms of transposons, their deregulation and different mechanisms underlying transposon-mediated carcinogenesis in humans focusing on the three most prevalent types, lung, breast and colorectal cancers, were reviewed. The modes of regulation employed include alternative splicing, deletion, insertion, duplication in genes and promoters resulting in upregulation, downregulation or silencing of genes.


Assuntos
Elementos de DNA Transponíveis/genética , Elementos de DNA Transponíveis/fisiologia , Neoplasias/genética , Expressão Gênica/genética , Regulação Neoplásica da Expressão Gênica/genética , Instabilidade Genômica/genética , Genômica/métodos , Humanos , Neoplasias/fisiopatologia , Sequências Repetitivas de Ácido Nucleico/genética , Retroelementos/genética
8.
New Phytol ; 233(1): 66-83, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34455592

RESUMO

The plant immune system protects against pests and diseases. The recognition of stress-related molecular patterns triggers localised immune responses, which are often followed by longer-lasting systemic priming and/or up-regulation of defences. In some cases, this induced resistance (IR) can be transmitted to following generations. Such transgenerational IR is gradually reversed in the absence of stress at a rate that is proportional to the severity of disease experienced in previous generations. This review outlines the mechanisms by which epigenetic responses to pathogen infection shape the plant immune system across expanding time scales. We review the cis- and trans-acting mechanisms by which stress-inducible epigenetic changes at transposable elements (TEs) regulate genome-wide defence gene expression and draw particular attention to one regulatory model that is supported by recent evidence about the function of AGO1 and H2A.Z in transcriptional control of defence genes. Additionally, we explore how stress-induced mobilisation of epigenetically controlled TEs acts as a catalyst of Darwinian evolution by generating (epi)genetic diversity at environmentally responsive genes. This raises questions about the long-term evolutionary consequences of stress-induced diversification of the plant immune system in relation to the long-held dichotomy between Darwinian and Lamarckian evolution.


Assuntos
Epigênese Genética , Imunidade Vegetal , Elementos de DNA Transponíveis , Regulação da Expressão Gênica de Plantas , Imunidade Vegetal/genética
9.
Methods Mol Biol ; 2387: 63-69, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34643902

RESUMO

Mycobacterium ulcerans is a slow-growing environmental bacterium that causes a severe skin disease known as Buruli ulcer. Identification of environmental reservoirs and agents associated with disease transmission is crucial to understanding the risk factors for this emerging infectious disease. Since culture of M. ulcerans from the environment still proves to be problematic, the direct detection of M. ulcerans in environmental samples via PCR has become increasingly important as the research community seeks to elucidate the mode(s) of transmission and environmental reservoir(s) of this elusive organism.


Assuntos
Mycobacterium ulcerans , Úlcera de Buruli/diagnóstico , Elementos de DNA Transponíveis , DNA Bacteriano/genética , Humanos , Mycobacterium ulcerans/genética , Reação em Cadeia da Polimerase em Tempo Real
10.
Methods Mol Biol ; 2387: 71-80, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34643903

RESUMO

Mycobacterium ulcerans is a slow-growing environmental bacterium that causes a severe skin disease known as Buruli ulcer. Rapid detection of M. ulcerans in clinical specimens is essential for ensuring early diagnosis and prevention of disability. This chapter describes a real-time PCR method for the direct detection of M. ulcerans from a variety of clinical and environmental samples (Fig. 1). Methods for the extraction of DNA from swabs, fresh tissue biopsies, and fixed tissue sections, which are the most common types of specimens used in the diagnosis of Buruli ulcer, are described in Chapter 6 . Chapter 7 describes the appropriate DNA extraction methods for environmental samples including soil, detritus, water, animal feces, and insects, as reliable detection of M. ulcerans in the environment is becoming increasingly important for understanding the ecology and transmission of this elusive pathogen.


Assuntos
Mycobacterium ulcerans , Animais , Úlcera de Buruli/diagnóstico , Elementos de DNA Transponíveis , DNA Bacteriano/genética , Mycobacterium ulcerans/genética , Reação em Cadeia da Polimerase em Tempo Real
11.
Methods Mol Biol ; 2377: 199-213, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709618

RESUMO

Transposon-directed insertion site sequencing (TraDIS) combines random transposon mutagenesis and massively parallel sequencing to shed light on bacterial gene function on a genome-wide scale and in a high-throughput manner. The technique has proven to be successful in the determination of the fitness contribution of every gene under specific conditions both in vitro and in vivo. In this contribution, we describe the procedure used for the identification of Escherichia coli K1 genes essential for in vitro growth, survival in pooled human serum and gastrointestinal colonisation in a rodent model of neonatal invasive infection. TraDIS has broad application for systems-level analysis of a wide range of pathogenic, commensular and saprophytic bacteria.


Assuntos
Escherichia coli , Elementos de DNA Transponíveis/genética , Escherichia coli/genética , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Mutagênese Insercional , Virulência/genética
12.
Methods Mol Biol ; 2377: 237-258, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709620

RESUMO

Transposon sequencing (Tn-seq) has greatly accelerated the rate at which gene function can be profiled in microbial organisms. This technique has been applied to the study of the dental caries pathogen Streptococcus mutans where it has been used to generate large transposon mutant libraries. Coupled with high-throughput sequencing and bioinformatics tools, culture of these transposon mutant libraries has facilitated the identification of essential and conditional essential genes. In this chapter, we describe a procedure for performing Tn-seq studies in S. mutans that covers pooled transposon mutant construction, in vitro culture, and DNA library sequencing and data analysis.


Assuntos
Genes Essenciais , Streptococcus mutans , Elementos de DNA Transponíveis/genética , Cárie Dentária , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mutagênese Insercional , Análise de Sequência de DNA , Streptococcus mutans/genética
13.
Methods Mol Biol ; 2377: 215-236, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709619

RESUMO

Identification of essential genes is key to understanding the required processes and gene products of organisms under one or more conditions. Transposon sequencing (Tn-seq) has been used to predict essential genes or ones that conditionally impact fitness in a wide variety of organisms. Here, we describe the generation of genome-scale mutant libraries and the analysis of Tn-seq data to identify essential genes from cultures grown in a single condition as well as those that are conditionally important by analyzing the behavior of these mutant libraries in different growth environments. While we illustrate the approach using data derived from Tn-seq analysis of the α-proteobacteria Rhodobacter sphaeroides and Zymomonas mobilis, the protocols and systems we describe should be generally applicable to a variety of organisms.


Assuntos
Biblioteca Genômica , Elementos de DNA Transponíveis/genética , Genes Essenciais/genética , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Mutagênese Insercional , Análise de Sequência
14.
Methods Mol Biol ; 2377: 259-271, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709621

RESUMO

A powerful method for examining genetic fitness and function on a large scale is to couple saturating transposon mutagenesis with high-throughput sequencing (TnSeq). By mapping where transposon insertions can be tolerated in a genome, it is possible to analyze the fitness of every gene in a genome simultaneously under a given growth condition. While this technique can describe genes as essential or nonessential under those growth conditions, sufficient mutagenesis and sequencing depth can provide more subtle differences in fitness. In this paper, TnSeq was used to analyze gene fitness of two Alphaproteobacteria from different environments: the freshwater oligotroph Brevundimonas subvibrioides (Caulobacterales) and the soil plant pathogen Agrobacterium tumefaciens (Rhizobiales) for the purpose of comparing conservation of gene function.


Assuntos
Genes Essenciais , Ciclo Celular , Elementos de DNA Transponíveis/genética , Sequenciamento de Nucleotídeos em Larga Escala , Mutagênese , Mutagênese Insercional
15.
Methods Mol Biol ; 2377: 303-315, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709623

RESUMO

Essential genes are those that are indispensable for the survival of organism under specific growth conditions. Investigating essential genes in pathogenic bacteria not only helps to understand vital biological networks but also provides novel targets for drug development. Availability of genetic engineering tools and high-throughput sequencing methods has enabled essential genes identification in many pathogenic gram-positive and gram-negative bacteria. Bacteroides fragilis is one of the major bacteria specific of human gastrointestinal microbiota. When B. fragilis moves out of its niche, it turns into deadly pathogen. Here, we describe detailed method for the essential gene identification in B. fragilis. Generated transposon mutant pool can be used for other applications such as identification of genes responsible for drug resistance in B. fragilis.


Assuntos
Genes Essenciais , Antibacterianos , Elementos de DNA Transponíveis/genética , Bactérias Gram-Negativas , Bactérias Gram-Positivas , Humanos
16.
Methods Mol Biol ; 2377: 273-302, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709622

RESUMO

Functional genomics of bacteria commonly aims at establishing genotype-phenotype links in microorganisms of industrial, technological and biomedical relevance. In this regard, random transposon mutagenesis coupled to high-throughput next-generation sequencing approaches, termed transposon-insertion sequencing (TIS), has emerged as a robust, genome-wide alternative to perform functional genome analysis. Though these approaches have been used in a large number of studies involving pathogenic and clinically relevant bacteria, they have received little attention in the fields of commensal and potentially beneficial bacteria, including probiotic microorganisms. In this chapter, we describe the implementation of the TIS method Transposon-Directed Insertion Sequencing to describe the set of essential genes in a representative strain of a genus encompassing several commensal and potentially probiotic bacteria and discuss considerations when applying similar methodological approaches to other Bifidobacterium species/strains of interest.


Assuntos
Bifidobacterium breve , Bifidobacterium breve/genética , Elementos de DNA Transponíveis , Genes Essenciais , Mutagênese
17.
Methods Mol Biol ; 2377: 391-421, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34709629

RESUMO

TnSeq, or sequencing of transposon insertion libraries, has proven to be a valuable method for probing the functions of genes in a wide range of bacteria. TnSeq has found many applications for studying genes involved in core functions (such as cell division or metabolism), stress response, virulence, etc., as well as to identify potential drug targets. Two of the most commonly used transposons in practice are Himar1, which inserts randomly at TA dinucleotides, and Tn5, which can insert more broadly throughout the genome. These insertions cause putative gene function disruption, and clones with insertions in genes that cannot tolerate disruption (in a given condition) are eliminated from the population. Deep sequencing can be used to efficiently profile the surviving members, with insertions in genes that can be inferred to be non-essential. Data from TnSeq experiments (i.e. transposon insertion counts at specific genomic locations) is inherently noisy, making rigorous statistical analysis (e.g. quantifying significance) challenging. In this chapter, we describe Transit, a Python-based software package for analyzing TnSeq data that combines a variety of data processing tools, quality assessment methods, and analytical algorithms for identifying essential (or conditionally essential) genes.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Algoritmos , Elementos de DNA Transponíveis/genética , Biblioteca Gênica , Genes Essenciais , Genômica , Mutagênese Insercional
18.
Cells ; 10(12)2021 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-34944084

RESUMO

Interspecific hybridization may lead to sterility and/or inviability through differential expression of genes and transposable elements (TEs). In Drosophila, studies have reported massive TE mobilization in hybrids from interspecific crosses of species presenting high divergence times. However, few studies have examined the consequences of TE mobilization upon hybridization in recently diverged species, such as Drosophila arizonae and D. mojavensis. We have sequenced transcriptomes of D. arizonae and the subspecies D. m. wrigleyi and their reciprocal hybrids, as well as piRNAs, to analyze the impact of genomic stress on TE regulation. Our results revealed that the differential expression in both gonadal tissues of parental species was similar. Globally, ovaries and testes showed few deregulated TEs compared with both parental lines. Analyses of small RNA data showed that in ovaries, the TE upregulation is likely due to divergence of copies inherited from parental genomes and lack of piRNAs mapping to them. Nevertheless, in testes, the divergent expression of genes associated with chromatin state and piRNA pathway potentially indicates that TE differential expression is related to the divergence of regulatory genes that play a role in modulating transcriptional and post-transcriptional mechanisms.


Assuntos
Elementos de DNA Transponíveis/genética , Drosophila/genética , Regulação da Expressão Gênica , Gônadas/metabolismo , Hibridização Genética , Animais , Feminino , Perfilação da Expressão Gênica , Células Germinativas/metabolismo , Masculino , Ovário/metabolismo , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Especificidade da Espécie , Testículo/metabolismo
19.
Cells ; 10(12)2021 12 20.
Artigo em Inglês | MEDLINE | ID: mdl-34944100

RESUMO

During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.


Assuntos
Elementos de DNA Transponíveis/genética , Domesticação , Genoma , Evolução Molecular , Dosagem de Genes
20.
Int J Mol Sci ; 22(24)2021 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-34948223

RESUMO

Insertions of transposable elements (TEs) in eukaryotic genomes are usually associated with repressive chromatin, which spreads to neighbouring genomic sequences. In ovaries of Drosophila melanogaster, the Piwi-piRNA pathway plays a key role in the transcriptional silencing of TEs considered to be exerted mostly through the establishment of H3K9me3 histone marks recruiting Heterochromatin Protein 1a (HP1a). Here, using RNA-seq, we investigated the expression of TEs and the adjacent genomic regions upon Piwi and HP1a germline knockdowns sharing a similar genetic background. We found that the depletion of Piwi and HP1a led to the derepression of only partially overlapping TE sets. Several TEs were silenced predominantly by HP1a, whereas the upregulation of some other TEs was more pronounced upon Piwi knockdown and, surprisingly, was diminished upon a Piwi/HP1a double-knockdown. We revealed that HP1a loss influenced the expression of thousands of protein-coding genes mostly not adjacent to TE insertions and, in particular, downregulated a putative transcriptional factor required for TE activation. Nevertheless, our results indicate that Piwi and HP1a cooperatively exert repressive effects on the transcription of euchromatic loci flanking the insertions of some Piwi-regulated TEs. We suggest that this mechanism controls the silencing of a small set of TE-adjacent tissue-specific genes, preventing their inappropriate expression in ovaries.


Assuntos
Proteínas Argonauta/metabolismo , Elementos de DNA Transponíveis , Proteínas de Drosophila/metabolismo , Células Germinativas/metabolismo , Ovário/metabolismo , RNA-Seq , Animais , Proteínas Argonauta/genética , Proteínas de Drosophila/genética , Drosophila melanogaster , Feminino
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